Sat Oct 8 18:44:23 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 18:44:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 497 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6207822 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -31.99500 17.65700 ymin,ymax (A): -23.75400 23.06100 zmin,zma (A): -12.52500 44.82200 x,y,z range (A): 49.65200 46.81500 57.34700 scale (grids/A): 0.6207822 object centre (A): -7.169001 -0.3465004 16.14850 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.53432 89.27116 89.80321 assigned negative charge : -387.4045 centred at (gu) : 88.43547 89.30170 89.68643 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6619 nv = 96 ne = 84 npr = 53802 no. pairs analyzed = 53802 no. exposed pairs = 2977 no. arc points = 21589 no. surface atoms = 1000 nbur = 1589 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3747 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.3000000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2113 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8141433E-09 1.0732697E-08 midg,1,midg; midg,igrid,midg 6.4109873E-09 1.1584339E-09 1,midg,midg; igrid,midg,midg -4.7580420E-09 7.2787221E-09 gauss-seidel spectral radius is 0.9865574 estimated iterations to convergence 71 setup time was (sec) 0.6000000 now iterating at: 18:44:24 rms-change max change #iterations 0.1290841 21.10263 at 10iterations 1.1898869E-02 1.711475 at 20iterations 1.1010317E-03 0.1708641 at 30iterations 1.0223970E-04 1.5678406E-02 at 40iterations 9.6384056E-06 1.3427734E-03 at 50iterations finished qdiffx linear iterations at : 18:44:28 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 9.6384056E-06 1.3427734E-03 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 18:44:28 4.397u 0.256s 0:04.93 94.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 18:44:28 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 497 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.862347 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -31.99500 17.65700 ymin,ymax (A): -23.75400 23.06100 zmin,zma (A): -12.52500 44.82200 x,y,z range (A): 49.65200 46.81500 57.34700 scale (grids/A): 1.862347 object centre (A): -7.169001 -0.3465004 16.14850 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.60239 87.81326 89.40942 assigned negative charge : -387.4045 centred at (gu) : 85.30618 87.90493 89.05907 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21589 grid for indexing accessible points = 1.400000 m= 25971 mr = 50496 m= 3679 mr = 19457 m= 206 mr = 2289 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 3418 time to turn everything in is 0.5600000 number of dielectric boundary points 29145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19253 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6207822 object centre at (A) : -7.169001 -0.3465004 16.14850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6938111E-02 2.5590928E-02 midg,1,midg; midg,igrid,midg 1.2719229E-02 2.2341020E-03 1,midg,midg; igrid,midg,midg -3.7357325E-03 2.9782493E-02 gauss-seidel spectral radius is 0.9985698 estimated iterations to convergence 210 setup time was (sec) 0.8900000 now iterating at: 18:44:29 rms-change max change #iterations 4.045800 189.4151 at 10iterations 1.859106 65.90229 at 20iterations 0.8549531 27.96861 at 30iterations 0.3922971 13.04203 at 40iterations 0.1816684 6.035709 at 50iterations 8.3455041E-02 2.917419 at 60iterations 3.8367085E-02 1.179783 at 70iterations 1.7742047E-02 0.5972996 at 80iterations 8.1126578E-03 0.2616472 at 90iterations 3.7526791E-03 0.1266298 at 100iterations 1.7266257E-03 5.2787781E-02 at 110iterations 7.9575833E-04 2.7981758E-02 at 120iterations finished qdiffx linear iterations at : 18:44:38 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 7.9575833E-04 2.7981758E-02 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 18:44:39 9.700u 0.255s 0:10.30 96.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 18:44:39 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 497 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.793520 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -31.99500 17.65700 ymin,ymax (A): -23.75400 23.06100 zmin,zma (A): -12.52500 44.82200 x,y,z range (A): 49.65200 46.81500 57.34700 scale (grids/A): 2.793520 object centre (A): -7.169001 -0.3465004 16.14850 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.40343 86.71973 89.11416 assigned negative charge : -387.4045 centred at (gu) : 82.95929 86.85736 88.58855 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 165583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21589 grid for indexing accessible points = 1.400000 m= 84726 mr = 121739 m= 29695 mr = 70369 m= 6528 mr = 24076 m= 824 mr = 4922 m= 60 mr = 541 m= 1 mr = 22 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 11672 time to turn everything in is 1.460000 number of dielectric boundary points 65749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 19631 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.862347 object centre at (A) : -7.169001 -0.3465004 16.14850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6206315E-02 0.3154477 midg,1,midg; midg,igrid,midg 0.1581036 1.0946931E-04 1,midg,midg; igrid,midg,midg -2.9989043E-02 0.3997895 gauss-seidel spectral radius is 0.9992343 estimated iterations to convergence 285 setup time was (sec) 1.810000 now iterating at: 18:44:41 rms-change max change #iterations 9.458026 412.7942 at 10iterations 5.427581 153.0092 at 20iterations 3.099474 71.45810 at 30iterations 1.764892 37.91790 at 40iterations 1.006556 18.59339 at 50iterations 0.5724488 11.05776 at 60iterations 0.3262294 5.961650 at 70iterations 0.1854010 3.504684 at 80iterations 0.1054333 1.994013 at 90iterations 5.9922226E-02 1.102348 at 100iterations 3.4120850E-02 0.6675205 at 110iterations 1.9368660E-02 0.3485962 at 120iterations 1.1011338E-02 0.2146339 at 130iterations 6.2759225E-03 0.1231451 at 140iterations 3.5696693E-03 7.5052261E-02 at 150iterations 2.0265379E-03 3.8772583E-02 at 160iterations 1.1554683E-03 2.0988464E-02 at 170iterations 6.5627816E-04 1.1997223E-02 at 180iterations finished qdiffx linear iterations at : 18:44:54 total time elapsed so far: 15.45000 # loops : 180 mean,max change (kT/e) : 6.5627816E-04 1.1997223E-02 energy calculations done at 15.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.62000 DelPhi exited at 18:44:55 15.622u 0.311s 0:16.20 98.3% 0+0k 0+0io 0pf+0w